chr5-130006612-G-A

Position:

• chr5-130006612-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175856.5(CHSY3):​c.1086+98252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,992 control chromosomes in the GnomAD database, including 8,236 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8236 hom., cov: 32)
• Consequence: CHSY3 NM_175856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

Genes affected

CHSY3 (HGNC:24293): (chondroitin sulfate synthase 3) CSS3 is a glycosyltransferase that has both glucuronyltransferase and N-acetylgalactosaminyltransferase activities (Yada et al., 2003 [PubMed 12907687]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHSY3	NM_175856.5	c.1086+98252G>A		intron_variant		ENST00000305031.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHSY3	ENST00000305031.5	c.1086+98252G>A		intron_variant		1	NM_175856.5	P1
CHSY3	ENST00000507545.1	n.275-45472G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49287 AN: 151874 Hom.: 8225 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.328

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49319 AN: 151992 Hom.: 8236 Cov.: 32 AF XY: 0.333 AC XY: 24715 AN XY: 74258

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.327

Alfa AF: 0.331 Hom.: 4017

Bravo AF: 0.316

Asia WGS AF: 0.427 AC: 1481 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6878100; hg19: chr5-129342305; COSMIC: COSV59274401;